[gmx-users] I have a problem with my biphasic system

[Justin Lemkul]

On 11/1/12 5:49 PM, Ali Alizadeh wrote:
> Dear All usres
>
>
> I have a system that contains water , methane and propane in 240 k and 300
> bar,
>
> My simulation box is rectangular .
>
> Water film is in middle of my box. Methane and propane is around it.
>
> I have a problem, my methane and propane molecules do not diffuse in water
> film(even my methane molecules),
>
> I do simulation, 30 nano second
>
> methane molecules = 834
> propane molecules = 92
> water molecules = 1656
>
> These links is related to md.mdp and .mdp for energy minimization
>
> http://trainbit.com/files/1132999884/md.mdp
> http://trainbit.com/files/2132999884/minim.mdp
>
>

The permissions on your files are set such that no one else can view them.

Why would you expect your alkanes to dissolve in water?  The solubility of 
methane is very small (roughly 0.02 g/kg of water at 25 C, or about 0.0014 M). 
Given this information, in your very small system, basically no methane 
molecules would ever partition into the water layer.  I didn't do the 
back-of-the-envelope calculations for propane, but you get the idea.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================